| Peptidylprolyl isomerase (EC 5.2.1.8) | FSU_2256 | C9RS13 | 1 |
| Peptidylprolyl isomerase (EC 5.2.1.8) | surA FSU_0941 | C9RLW8 | 1 |
| Peptidylprolyl isomerase (EC 5.2.1.8) | cypD SCH_0494 | Q57SB1 | 1 |
| Peptidylprolyl isomerase (EC 5.2.1.8) (Fragment) | VSAK1_02439 | A6D9K3 | 1 |
| Periplasmic alpha-amylase | malS VSAK1_14485 | A6D4T2 | 1 |
| Periplasmic binding protein, putative | SAOUHSC_00074 | Q2G1N4 | 1 |
| Periplasmic binding protein/LacI transcriptional regulator | B195_09182 | M5R0V3 | 1 |
| Periplasmic binding s and sugar binding domain of the LacI family protein | HPSD74_0738 | U4SKG8 | 1 |
| Periplasmic dipeptide transport protein | VS_0075 | B7VH98 | 1 |
| Periplasmic dipeptide transport protein (Dipeptide-binding protein) (DBP) | dppA b3544 JW3513 | P23847 | 1 |
| PERIPLASMIC DIPEPTIDE TRANSPORT SUBSTRATE-BINDING PROTEIN | dppA jhp_0283 | Q9ZMD7 | 1 |
| Periplasmic glycerophosphodiester phosphodiesterase (EC 3.1.4.46) | glpQ STM2282 | Q8ZNG7 | 1 |
| Periplasmic iron-binding protein (Fragment) | fbp | Q50988 | 1 |
| Periplasmic L-asparaginase II | ansB FTN_0555 | A0Q5D5 | 1 |
| Periplasmic L-asparaginase II (EC 3.5.1.1) | ansB STM3106 | Q7CPT7 | 1 |
| Periplasmic L-asparaginase II (EC 3.5.1.1) | ansB FTT_0464 | Q5NHJ0 | 1 |
| Periplasmic maltose-binding protein | malE KPN_04423 | A6TGU4 | 1 |
| Periplasmic molecular chaperone for outer membrane proteins | hlpA KPN_00191 | A6T4Y0 | 1 |
| Periplasmic nitrate reductase (EC 1.7.99.4) | napA VS_II0598 | B7VRL0 | 1 |
| Periplasmic nitrate reductase (EC 1.7.99.4) | napA PA1174 | Q9I4G3 | 1 |
| Periplasmic nitrate reductase (EC 1.7.99.4) | napA SSON_2264 | Q3Z001 | 1 |
| Periplasmic nitrate reductase (EC 1.9.6.1) | napA SCH_2264 | Q57M92 | 1 |
| Periplasmic nitrate reductase, electron transfer subunit (Diheme cytochrome c NapB) | napB Cj0783 | Q0PAA7 | 1 |
| Periplasmic oligopeptide-binding domain protein (Fragment) | HPSD74_2260 | U4SNB2 | 1 |
| Periplasmic oligopeptide-binding protein | VS_0990 | B7VLU9 | 1 |
| Periplasmic oligopeptide-binding protein | oppA STM1746 | P06202 | 1 |
| Periplasmic oligopeptide-binding protein | oppA YPO2182 | Q7CIN4 | 1 |
| Periplasmic pH-dependent serine endoprotease DegQ (EC 3.4.21.107) (Protease Do) | degQ hhoA b3234 JW3203 | P39099 | 1 |
| Periplasmic protein involved in polysaccharide export | VS_1521 | B7VNV8 | 1 |
| Periplasmic protein involved in polysaccharide export | NSU_1111 | G6E9U0 | 1 |
| Periplasmic sensory protein associated with the TorRS two-component regulatory system | VSAK1_14697 | A6D7F0 | 1 |
| Periplasmic serine endoprotease DegP-like (EC 3.4.21.107) | htrA S0156 SF0153 AJR25_013775 | A0A0H2VSZ0 | 1 |
| Periplasmic serine endoprotease DegP-like (EC 3.4.21.107) | htrA SCH_0209 | Q57T46 | 1 |
| Periplasmic serine endoprotease DegP-like (EC 3.4.21.107) | degQ SCH_3286 | Q57JC0 | 1 |
| Periplasmic serine protease Do, heat shock protein | degP KPN_00176 | A6T4W5 | 1 |
| Periplasmic serine protease, DO/DeqQ family (EC 3.4.21.-) | MXAN_4330 | Q1D4B9 | 1 |
| Periplasmic solute binding family protein | mntC HPSD74_1047 | U4SI88 | 1 |
| Periplasmic solute binding family protein | FTT_0209c | Q5NI74 | 1 |
| Permease IIC component | LMRG_02229 | A0A0H3GNS6 | 1 |
| Permease YjgP/YjgQ family protein | PP_0982 | Q88P71 | 1 |
| Permease YjgP/YjgQ family protein (EC 3.6.3.-) | FTT_1319 | Q5NFC0 | 1 |
| Permease YjgP/YjgQ family protein (EC 3.6.3.-) | FTT_1320 | Q5NFB9 | 1 |
| Peroxiredoxin (Alkyl hydroperoxide reductase C) | B195_11176 | M5QIY8 | 1 |
| Peroxiredoxin like protein | SC1083_1486 | G4A9H2 | 1 |
| Peroxiredoxin of the AhpC/TSA family | Fphi_1627 | B0TZT9 | 1 |
| Peroxiredoxin OsmC (EC 1.11.1.15) (Osmotically-inducible protein C) | osmC b1482 JW1477 | P0C0L2 | 1 |
| Peroxiredoxin, AhpC-TSA family protein | Fphi_1918 | B0TZV4 | 1 |
| Peroxiredoxin, AhpC-TSA family protein | FTN_0958 | A0Q6I1 | 1 |
| Peroxiredoxin, alkylhydroperoxide reductase-small subunit (EC 1.11.1.15) | ahpC PP_2439 | Q88K52 | 1 |
| Pertussis toxin subunit 1 (PTX S1) (Islet-activating protein S1) (IAP S1) (NAD-dependent ADP-ribosyltransferase) (EC 2.4.2.-) | ptxA BP3783 | P04977 | 1 |
| Pertussis toxin subunit 2 (PTX S2) (Islet-activating protein S2) (IAP S2) | ptxB BP3784 | P04978 | 1 |
| Pertussis toxin subunit 3 (PTX S3) (Islet-activating protein S3) (IAP S3) | ptxC BP3787 | P04979 | 1 |
| Pertussis toxin subunit 4 (PTX S4) (Islet-activating protein S4) (IAP S4) | ptxD BP3785 | P0A3R5 | 1 |
| Pesticin | pst YPPCP1.05c | Q57159 | 1 |
| Pgm protein | pgm KPR_3868 | R4YD15 | 1 |
| Pgt1 | pgt1 | A0A0E3TIJ9 | 1 |
| pH 6 antigen (Adhesin) (Antigen 4) | psaA YPO1303 y2882 YP_1289 | P31522 | 1 |
| Phage capsid protein | B195_21440 | M5QE44 | 1 |
| Phage holin, lambda family | PP_3884 | Q88G42 | 1 |
| Phage shock protein A | pspA CPC_1811 | B1BGD9 | 1 |
| Phage shock protein A | pspA SF1309 S1391 | P0AFM8 | 1 |
| Phage shock protein A | VSAK1_01072 | A6D582 | 1 |
| Phage shock protein A homolog | ydjF BSU06180 | P54617 | 1 |
| Phage shock protein E | VSAK1_01517 | A6D2I9 | 1 |
| Phage shock protein G | pspG yjbO b4050 JW5716 | P32696 | 1 |
| Phage shock protein: activates phage shock-protein expression | pspC KPN_01299 | A6T811 | 1 |
| Phage spanin Rz LysB | SS52_2987 | A0A0F6F8V1 | 1 |
| Phage tail collar domain protein | MXAN_0326 | Q1DFH2 | 1 |
| Phage tail fiber protein | SS52_2979 | A0A0F6F8U3 | 1 |
| Phage tail sheath protein | SAMEA3375004_00263 | A0A1Q9BL85 | 1 |
| Phage tail tape measure protein, family | AC3_1424 | B1BUA6 | 1 |
| Phage-like element PBSX protein XkdF | xkdF BSU12600 | P54326 | 1 |
| Phage-like element PBSX protein XkdK | xkdK BSU12650 | P54331 | 1 |
| Phage-like element PBSX protein XkdO | xkdO BSU12680 | P54334 | 1 |
| Phenazine biosynthesis protein PhzB 2 | phzB2 PA1900 | Q9S508 | 1 |
| Phenylalanine 4-monooxygenase (EC 1.14.16.1) | phhA B195_08407 | M5QJF8 | 1 |
| Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase alpha subunit) (PheRS) | pheS spr0507 | Q8DQT8 | 1 |
| Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase alpha subunit) (PheRS) | pheS SF1517 S1634 | Q83L37 | 1 |
| Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase alpha subunit) (PheRS) | pheS PA2740 | Q9I0A3 | 1 |
| Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase alpha subunit) (PheRS) | pheS HPSD74_0119 | U4SN60 | 1 |
| Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase alpha subunit) (PheRS) | pheS SPy_0768 M5005_Spy0587 | Q9A0I1 | 1 |
| Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) | spr1726 | Q8DNH2 | 1 |
| Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase beta subunit) (PheRS) | pheT YPO2428 y1909 YP_2215 | Q8ZDX1 | 1 |
| Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase beta subunit) (PheRS) | pheT HPSD74_0118 | U4SPE7 | 1 |
| Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase beta subunit) (PheRS) | pheT SPy_0769 M5005_Spy0588 | Q9A0I0 | 1 |
| PhnI protein | VSAK1_19819 | A6CWP4 | 1 |
| PhnM protein | VSAK1_19839 | A6CWP8 | 1 |
| Pho4 family protein | VSAK1_05005 | A6D324 | 1 |
| PhoH family protein, putative ATPase | FTN_1064 | A0Q6T6 | 1 |
| PhoH-like protein | phoL spr0849 | Q8DQ46 | 1 |
| PhoH-like protein | ybeZ b0660 JW0657 | P0A9K3 | 1 |
| PhoH-like protein | CD630_24411 | Q182C7 | 1 |
| PhoP regulated: reduced macrophage survival | pagC SCH_1256 | Q57Q49 | 1 |
| Phosphate ABC transporter, periplasmic phosphate-binding protein | pstS MXAN_4788 | Q1D323 | 1 |
| Phosphate ABC transporter, periplasmic phosphate-binding protein, putative | VSAK1_15692 | A6D4P9 | 1 |
| Phosphate acetyltransferase (EC 2.3.1.8) | pta FSU_1793 | C9RQT8 | 1 |
| Phosphate acetyltransferase (EC 2.3.1.8) (Phosphotransacetylase) | pta FTN_0126 | A0Q472 | 1 |
| Phosphate acetyltransferase (EC 2.3.1.8) (Phosphotransacetylase) | pta KPN_02688 | A6TBY4 | 1 |
| Phosphate acetyltransferase (EC 2.3.1.8) (Phosphotransacetylase) | pta SF2373 S2508 | P0A9M9 | 1 |
| Phosphate acetyltransferase (EC 2.3.1.8) (Phosphotransacetylase) | pta PA0835 | Q9I5A5 | 1 |